29 August 2014

I used to be a big proponent of putting a lot of stuff online for students.

After two upgrades to learning management systems, where most of the class material I worked hard on was damn near impossible to import into the new system, I am considerably less enthusiastic. Everyone has a limit to how many times they are willing to key in the same stuff. Again.

25 August 2014

By this time next year, I’m going to need a new cover. The University of Texas-Pan American won’t exist any more. It will be abolished and replaced by University of Texas Rio Grande Valley. (And that name won’t fit on an iPad cover, either, darn it.)

Today is the first day of the fall semester, and it is a little bittersweet knowing that this is the start of the last year for this university. I’ve heard quite a few people already talking about it. But while some people have been a little bummed, a common refrain I’ve heard is:

I was having a discussion last week with some colleagues who are not in the sciences about their publishing experience. The conversation echoed an online one I had with Rebecca Schulman on Twitter after she published an article in Slate about academic publishing. The academic publishing process she described was not one I recognized. I barely recognized the publishing process in the chat last night, either.

This individual described the process of submitting to a reputable business journal.

Start with a non-refundable $350 submission fee.

Don’t expect any reviews in less than six months. In fact, even six months is optimistic.

If your manuscript is given a recommendation of “revise and resubmit,” that will cost you another $150 submission fee.

I hear the litany of complaints above, and it seems to me that this is a ripe opportunity for an academic publisher. Surely someone can provide a better service to scholars than this. I wonder, “Where is the answer to PeerJ for business, the humanities, and other academic disciplines?”

The answer to why new journals are having a tough time breaking into those market, of course, is “prestige.” Certain journals were viewed as “the best” (suspected translation: high Impact Factor) which means people will put up with a huge amount of inconvenience and strife to get published in them.

We scientists may whinge about our journals, but they seem to be doing a better job across the board than in other academic fields. There are exceptions (grrr), but there are recognized as exceptions. Scientists have been slowly changing how academic publishing is done. And yes, it’s been too slow and too little, but we’ve made progress. We need to keep pushing so that our colleagues in other departments and colleges will have some of the same options in publishing that we are starting to enjoy.

Additional, 20 September 2014: There is a very interesting comparison of open access issues in sciences and humanities here. Hat tip to Mike Taylor.

Information and data included in abstracts presented at the SfN annual meeting are embargoed until the conclusion of the presentation or SfN press conference. Coverage of an abstract, poster, lay summary, data, or supplemental material, is strictly prohibited until the embargo is lifted.

The SfN has consistently been tone deaf when it comes to the scientific community online and social media. Their choices for official conference bloggers have repeatedly been baffling (see here from 2010 and here for 2011).

Their policies about “no photos from the poster session floor” are both unenforced and unenforceable, and people tweet pictures of their poster all the time. (I wrote this post over at Better Posters using pictures that members tweeted.)

The main conference page has this big heading about “Protecting Your Science at Neuroscience 2014.” This raises the question:

Protecting the science from whom?

What are the “wrong hands” that SfN is worried about conference results falling into? What nefarious individuals must be kept away from new neuroscience information? And how is someone’s research “protected” by an embargo that only lasts until the end of a presentation?

Let’s say that I was giving a talk at Neuroscience, and someone breaks the embargo with a tweet. How will SfN enforce their communication policy? What will be the consequences? I suspect the answer is, “None.” This makes this policy toothless and subtly encourages rule breaking.

I used to think that a reason for being a little circumspect about distributing conference materials outside the walls of a conference was to avoid running afoul of the Ingelfinger rule: journals won’t publish results that have already been published elsewhere. This tweet from SfN implies this.

Letting someone snap a photo of your poster might seem harmless, but it could hurt chances of being published.

But I have never, ever heard of a single case of a researcher who got burned and had their manuscript rejected because information from their conference presentation was mentioned online.

Here are just a few articles on the advantages of tweeting from conferences. There are many more that I know I am missing; let me know of others and I will add them!

With all the advantages these articles outline, what are these deep dark disadvantages SfN apparently sees that we don’t, that are so bad to warrant stopping up the flow of conversation?

Additional, 22 August 2014: Ivan Oransky has a post describing social media embargoes at another conference, Cold Spring Harbor Laboratory meetings. It is interesting to compare CSHL to SfN in this regard.

The motivation for CSHL’s policy is up front. SfN’s reasoning is obscure.

CSHL’s policy is “transparent and clear.” SfN’s is confusing (“Wait, can I tweet now?”)

CSHL’s policy “tries to evolve.” SfN’s seems to be completely top down and unresponsive.

I recently wrote a slightly whinging blog post about the time I spent updating all my online profiles after I had my most recent paper published. To my surprise, that experience got mentioned in a recent news article in Nature. It’s a sidebar that only appears in the online version of the story, not the print version, alas.

It’s a good reminder that when you write in public, you never know where your influence stops.

I•Con was a fan run science fiction convention in Victoria, British Columbia. There are several SF conventions with that name, but in this case, “I” was supposed to stand for “Island”, as in Vancouver Island.

There were two iterations of I•Con, and I was involved in organizing the second one, in October 1991. I was the art show director, helped get Barry Beyerstein invited as a science guest, and did miscellaneous other things, including designing the logo you see above.

This logo was initially designed on a Radio Shack Color Computer 3, with software called CoCo Max 2 (I think). You can tell the age of the software from the “spray can” pixels that make up the “2”.

The shape of the “2” was inspired by the Lethal Weapon 2 logo. I’m still a little surprised by that, because I’d hated Lethal Weapon 2 so much that I am surprised that I would life anything at all from that.

I used the Roman numerals because I liked the repetition of the shape of the “I” in I•Con and the “II” in the numerals.

When I made it, I considered this a success because it was about 90% of what I envisioned in my head.

Looking at it now, there is a little too much going on in the logo. Having both the Arabic and Roamn numerals is a little bit of overkill. It probably does not need the horizontal line between the word and the number.

Summary

For their great commercial importance as a human food delicacy, crayfish are now becoming of wider interest to molecular biologists, and also to conservationists due to the fact that in some countries many of the native crayfish species are under threat from human activity, disease, and competition from other introduced crayfish species. Helmed by three editors in Japan, Europe, and the US, this book invites contributions from experts around the globe, covering the conservation status and biology of all endangered species, taxonomy, and distribution of crayfishes worldwide.

In addition to helping with the editing, my name appears on a couple of chapters, too.

It’s slated for release early in 2015. Start recommending to your libraries and saving for your own copies today!

Larva of Crab. Second stage. Larva of Crab. First stage. they are then about half a line in length. Soon after exclusion this larva casts off its envelope and assumes the appearance represented in Jig. 139., which closely corresponds with that zoeaeiform Crustacean whose further changes were witnessed by Thompson, and which he had assured himself was an early or larval state of a common crab.The last form which immediately precedes the assumption of the mature characters corresponds, according to Thompson, with that of the genus Megalopa. The additional evidence adduced, in 1839, by Capt. Du Cane in proof of the actual metamorphosis of the Crustacean in question, was most acceptable. He affirms a corresponding metamorphosis to occur in the ditch-prawn (Palemon variabilis) and common shrimp (Crangon vulgaris). Dr. Thompson has witnessed similar metamorphoses in the genera Palinurus, Squilla, Pagurus, Porcellana, Galatea, and the marine species of Astacus, as well as in Palemon and Crangon.

Photo by Internet Archive Book Image on Flickr; used under a Creative Commons license.

Update, 13 August 2014: A couple of other journals in the same market as Science Advances (online, open access) have made a couple of interesting announcements today.

eNeuro is specifically soliciting for“Negative Results, Failure to Replicate, and Confirmation.” This is important, because replications are difficult to publish, but important.

eLife has just announced “Research advances”, which lets authors publish “significant
additions” to their articles that are already out.

I like these. The more journals try these sorts of innovations, the faster they might be able to shake the label of being Zune journals. Will Science Advances try anything this innovative?

And while I’m here, note that a $3,000 sticker price for the default options (less than 10 page article, more restrictive copyright license) makes Science Advances one of the more expensive open access journals. I’ve placed it on the graph seen on this site.

Our own experience as both scientists and teachers suggests to us that the problem begins with, and may be partially solved by, education.

Particularly at the early career stages, it is not surprising to find people do not understand some of the academic norms.

At a workshop that we ran in April this year, involving mainly PhD students and early career postdocs from a wide range of universities, we asked participants to complete a questionnaire on misconduct. Sixty-eight of them answered 51 questions to rate their perception of the severity of different kinds of questionable, unethical and fraudulent research practices, from zero (not really a problem) to three (severe, deserving censure and punishment).

We were relieved to find that most (96 per cent) of them rated “deliberately making up some or all of the data in a manuscript submitted for publication” as three (don’t ask about those 4 per cent who didn’t!). However, we were dismayed that only 54 per cent gave a three to “knowingly selecting only those data that support a hypothesis” and 42 per cent to “deleting some data to make trends clearer”. The naivety is staggering.

From grad students, this might be expected. From postdocs, not so much. I wonder what the scores would be from working professors.

But now, 20-plus years later, it is only fair to ask: Does (responsible conduct of research training) work? The simple answer is, “No.”

Education and training can be very effective at combating mistakes due to ignorance. But I doubt ignorance is the major reason for ethical lapses.

I would point to something both the Times Higher Ed and The Scientist articles bring up: competition. Here is something I tweeted during my time as the curator of the Real Scientists Twitter account. The quote is from Jeff Alexander, who was lead designer on Legend of the Five Rings and saw its tournament scene.

In intense competition with few prizes, people will want to quit the game. But what if they can’t quit the game? People who have invested a lot of time and effort into this may conclude that they have no chance playing by the established rules. Is it any surprise people will cheat?

If we want to deal with research misconduct, we need to change the incentive structures in scientific research.

Additional, 12 August 2014: From Neuroskeptic, in reaction to this post:

You can't teach people to be ethical. Not adults, anyway. Ethics is not a skill you get from attending the right Powerpoint presentations.

I disagree a bit here. I think you can teach people to be ethical, but:

06 August 2014

Yesterday, a single tweet announced that Kent Anderson would be the publisher for the American Association for the Advancement of Science (AAAS). This has now been confirmed by AAAS (longer press release here). I would like to congratulate Anderson for landing what must be a plum gig.

And I wish AAAS luck, because they will need it.

Anderson has a lot of knowledge about the scientific publishing industry, that much is clear. He has served as president of the Soceity for Scholarly Publishing.

But he also has a definite point of view about scientific publishing, which he has puts forward at the blog The Scholarly Kitchen. If I may try to summarize some of his positions (The Scholarly Kitchen is a group blog, so I may be misremembering other people’s positions as his; correct me if I’m wrong):

Anderson argues that subscription journals by “for profit” publishers is the One True Path of scientific publishing. This, he says, is the only method of disseminating scientific information that has been sustainable (e.g., here).

He has been critical of open access publishing. (Honestly, I wonder if he has a voodoo doll wearing a PLOS ONE t-shirt.) In this interview, he says, “I think (open access) is structurally flawed.”

He has been extremely critical of PubMed directing traffic away from publishers (e.g., here and here). That huge numbers of working biomedical scientists find PubMed invaluable to their research and use it every day seems not to matter much in Anderson’s point of view.

At every turn, Anderson had advocated positions that favour the interests of publishers over either the needs of working scientists or the general public.

It’s okay to have a point of view. It’s okay to defend publishers (I do it myself sometimes.) But it seems odd to put Anderson, for-profit publisher booster, in charge of the publishing arm of not-for-profit, member-driven scientific society, particularly at a time when the society is launching open access journals. Anderson has a reputation, and it’s not of someone who is interested in innovative publishing.

Anderson’s appointment is not a good move, public relations wise, for AAAS. But it will give other publishers an opportunity to contrast their positions with those espoused by Anderson. What publishers will support giving researchers and readers valuable tools that they want?

I once thought that Science magazine was rife for takeover by its members to become an open access journal. Anderson’s appointment seems like an open access takeover is exactly what AAAS fears, and they want someone to dig a moat and man the barricades.

Edit: Struck “for profit” in a couple of places, as the subscription model is probably more central to Anderson’s argument. And, as noted in the comments, Anderson has worked with non-profits.

05 August 2014

This annoys me so much. It presumes “quality” can be judged immediately and accurately, and that researchers should all be of the same mind about what the “right” research questions to ask are.

I wonder if, in other fields of creative endeavor, people write editorials calling for less work. “People are releasing more songs than ever, but have you noticed that there are still only 52 number one songs on Billboard magazine each year? We haven’t had any increases in number one songs since the 1950s!”

Would anyone ask a musician, “Why don’t you just write hits?” without expecting to get punched in the face? No, because there is some understanding that not everything is going to be a hit.

“Uncited research” is research that has not been cited yet. This is a great strength of scientific literature: you can go back and look at the old stuff. Some projects have “long tails,” and it’s not possible to know when someone will stumble across something you have created and find out something relevant to what they are doing. For example, Hill (1979) was not cited for almost two decades. Failure? Maybe. But because there is no statute of limitations on when we can cite papers, it eventually was cited. (Yes, I’ve cited it.)

Scientific papers are love letters to the future. We write them in hope that not only will they be useful within the first few years of publication, but that they may be useful to researchers living long after we are not.

Some works will only reach a small audience. That does not automatically make them less worthy, or less influential.

To use the music analogy again:

In 1968, The Velvet Underground were releasing records that very few people bought. But their work lasted, and regularly shows up on “Best of all time” lists.

In comparison, the 1968 Grammy winner for Record of the Year that year was “Up, Up, and Away.”

It’s a breezy, catchy, even memorable tune, but... I bet it doesn’t show on on many “Best of all time” lists now. I wager not many people would know the name of the band now.

This in turn leads to the bane of every scientist's existence: far too many papers to read in far too little time.

Not my bane. It has never been easier for me to find papers that are relevant to my interests, thanks to Google Scholar and similar tools.

One reason is the rise of author-pays open-access publishing. This has the benefit of allowing anyone to read the research in question without paying the publisher, but also has the disadvantage of giving publishers a strong commercial incentive to issue as much content as possible. ...

(S)ubscription business models at least
help to concentrate the minds of publishers on the poor souls trying to
keep up with their journals.

Subscription publishers have incentives to publish more scientific
literature, just like open access publishers do. If each journal tends
to be profitable, then you have incentive for publishers to make more
journals. The more journals they can put in their “big deal” packages,
they more they might make.

The incentive to publish is not coming from publishers. The incentive to publish comes from administrations, funding agencies, hiring committees, tenure and promotion committees. They all count publications. This seems indisputable. Indeed, the article goes on to make to admit this:

On one hand funders and employers should encourage scientists to issue smaller numbers of more significant research papers. This could be achieved by placing even greater emphasis on the impact of a researcher's very best work and less on their aggregate activity.

How are we going to evaluate “best” work? Unfortunately, the typical way that “very best work” is evaluate now is the journal Impact Factor (van Dijk et al. 2014). The problems of using Impact Factor to assess individual work are many, to put it mildly (Brembs et al. 2013).

In the end, we get a bait and switch! Instead of what the piece initially calls for (publish less), it ends with a call to publish even more. Now we are supposed to publish data in addition to our papers:

On the other they should require scientists to share all of their results as far as practically possible. But most of these should not appear in the form of traditional scholarly papers, which are too laborious for both the author and the reader to fulfil such a role. Rather, less significant work should be a issued in a form that is simple, standardised and easy for computers to index, retrieve, merge and analyse. Humans would interact with them only when looking for aggregated information on very specific topics.

So the issue is filter failure, not information overload.

Whatever the shortcomings of traditional journal articles are, they realize the awesome power of narrative. This is, I think, the reason why scientific journals have never just published the data, as I wrote before:

If science is purely and solely about “the facts,” why do we publish scientific papers at all? Why not just upload methods and datasets? If you have the data and the methods to generate them, isn’t that all you need to assess the “facts” in play?

(T)here is an inherent connection between stories and experimental science: they are both about causes. A satisfying story is built around causal connections. Without those causal connections, you have a series of disconnected events that makes about as much sense as a random inkblot.

If we struggle with too many papers now, we will struggle even more with too many datasets.

If you look closely, you can figure out what city this little guy is from.

When I tweeted this picture on the Real Scientists, someone claimed this has “the wrong number of legs.” Maybe. Maybe this little guys lost some in a fight or an accident, and is regenerating them. Or maybe this is actually a squat lobster, which usually tuck the last pair of legs (which are tiny and not used for walking) under their tail.

02 August 2014

As I mentioned earlier, my parents got to be voice actors for Sharknado 2: The Second One. (They screamed.) I also got to name sharks in the film. The request for the names, as it happened, came exactly on my parents’ fiftieth wedding anniversary (!), so I named my sharks after my parents.

I was excited when I opened up the email and saw the image of the first shark! Wow! It’s a shark that’s part of a celebrity cameo! Kelly Ripa is dispatching my mon’s shark on Live with Kelly and Michael!

Kelly retweeted a picture of this during the first showing of Sharknado 2.

Then I opened up the next email to see the image of the shark I named after my dad. I am pretty sure you will have to click to enlarge:

... I hoped that this wouldn’t lead to any conflicts in my parents’ household. But I got this email:

01 August 2014

When I recently published a paper (full text on DoctorZen.net) about finding a sand crab (Lepidopa websteri) where it hadn’t been before, I wrote about the images of the crab I found in a nature center. But I got thinking about how this crab has been shown in scientific papers.

The scientific literature on this crab is the almost only place where you will find images of it. A search of Google Images reveals only one page with pictures of the species (a googlewhack!) and that’s in the larval state. There are no pictures of adults except my own blog posts.

Because this species is obscure, I was able to do something that you can’t do very often: compile what may be absolutely every image of the species shown in the scientific literature. Click to enlarge:

It’s fascinating to compare the different images, for their use of technology, and the pros and cons of each representation.

Benedict 1903: The carapace is prominent and easy to see, but while this line drawing is clear, it ignores most of the animal.

Hay and Shore 1918: The black and white photograph is frustrating, because in the text, they note:

Color, in alcohol, probably also in life, pure white, but everywhere beautifully iridescent, giving pearly reflections at every turn of the body.

I read that description and I want something so much more than the picture of a damaged individual! I want to see the beautiful colours they are writing about! In fairness, the original picture on paper may be better than the scan shown here, but it would still be black and white.

Pearse et al. 1942: This picture may be the most elegant representation of L. websteri from an artistic point of view. There is some beautiful brush and ink work on display here. And while I wish the species name was set in italics, I am still attracted to the handmade warmth of the letters.

Scientifically, though, there’s one big mistake.

The caption lists the appendages below as the five walking legs. Nope. The first one, over on the left, is one of the mouthparts, not a leg. I know why this happened, though: this crab is a relative of hermit crabs (infraorder Anomura). All the crabs in this group share a feature: their fifth pair of walking legs are very small, and in sand crabs, tucked underneath the tail.

Boyko 2002: Technology has moved on. You can see an incredible increase in the level of detail and precision in these images, facilitated by digital cameras and graphics software. These images are invaluable for identification and technical work. They are very much in line with the sort of represented used by Benedict back in 1903.

But they show an “exploded” animal, with none of the parts in relation to each other, and no images of the prominent antennae.

World Birding Center 2009: I’m cheating a little, because this picture isn’t in the scientific literature. But it is in a professional nature center and museums generally strive for images that are scientifically accurate and engaging. This one is... neither. It looks like it was drawn from a very old specimen preserved in alcohol, or other images, rather than a living animal.

Faulkes 2014: These are, as far as I know, the first colour photographs on an adult L. websteri in the scientific literature, or even the Web. Now, you can finally get a sense of the beautiful pink overtones and iridescence that Hay and Shore mentioned.

The other thing I’m happy about with this figure is that it shows the whole, live animal, with everything in context. You can get a sense of the very first thing I noticed about this animal, which helped me recognize instantly that it was something different: the length of the antennae.

Update, 16 June 2016: Found a wonderful photograph of this species on Flickr. It’s much better than my own. I think it was taken after mine (February 2014) but posted before my paper was published. I can’t embed it here because it does not have a Creative Commons license.